THE EDITOR’S RESPONSE
I contacted the editor-in-chief of Proteomics, Michael Dunn, to find out more about what happened. Many scientists have speculated publicly that the peer review process went seriously wrong for this paper. Dunn assured me that the paper was reviewed by two “well-respected and highly competent reviewers” both of whom recommended minor revisions. For some reason, though, “neither picked up the references to creationism, nor did they recognize that sections of the text were plagiarized,” according to Dunn. It is not too surprising that the reviewers missed the plagiarism, but the title and abstract should have raised huge red flags warning the reviewers that this article had questionable science. I have to conclude that the reviewers were very sloppy, incompetent, or both; at the very least they were inattentive in this case, despite the editor’s claims to the contrary. And Dunn himself is not without responsibility in this case: he must have seen the reference to “the soul” in the article’s title, and he should have been more pro-active. His failure to make any public statement about the creationist claims in the article also raises questions about the leadership at the journal.

CONCLUSION
This entire episode points out a weakness in scientific peer review that creationists and other pseudoscience proponents may try to exploit again. We only caught this attempted fraud thanks to the diligence of bloggers: the journal itself had already missed it. What is perhaps more troubling is the fact that the journal relied solely on the plagiarism to force the retraction: if not for that, the article might have been published despite its unsubstantiated creationist claims. I asked Dunn specifically about this issue, but he declined to comment. The Warda and Han paper demonstrates a new strategy that proponents of creationism might attempt again, and perhaps next time they will not be so foolish as to plagiarize their text. We can only hope that the publicity surrounding this incident will alert both reviewers and editors of scientific journals to be on the lookout for “stealth” creationist claims in the future.

The title of the paper was “Mitochondria, the missing link between body and soul: Proteomic prospective evidence.” I’m still baffled by the fact that “well-respected and highly competent reviewers” could completely overlook the title and an abstract that makes extravagant claims for a complete and rather revolutionary revision of the most widely accepted explanation for the origins of mitochondria.

Creationists’ goal is to prove there’s a soul
That’s impossible to have evolved;
The task is quite trying; instead, they keep lying,
And think that their problem is solved.
These pinhead god-floggers just woke up the bloggers
Who slapped them back down to their place;
With options now fewer, they’ll try something newer;
A godly stupidity race.

It is a definite cause for great concern since the question must now be asked, How many articles besides this one have made it into print with a similar lack of attention paid to the text? .
Even papers that are done by people of integrity must needs be subjected to the peer review process in order to maintain high standards.
I suspect the cretinists will trot out this error for quite sometime.

You have it wrong, Grady. This is not Orwellian censorship. We in science have a responsibility to maintain standards and make sure that scientists stick to methodological naturalism. When researchers do not stick to naturalism, they are making unverifiable claims that slam the door on honest inquiry.

And in any case, mentioning the “soul” was not the reason this article was retracted, but because it engaged in plagiarism.

Reminds me of Orwells 1984 where the writer Syme went to a camp because he allowed the word “God” to be mentioned.

Naw. The pseudoxian Death Cultists are decidely Dark Age era. They have lists of demons to hate and fear and they persecute them and occasionally kill them whenever and however they can.

It must be tough to be an atheist in Texas
Category: Godlessness

Just ask Richard Mullens, who has not said he is an atheist, but was suspected of being one?and lost his job as a teacher for that reason.

Richard Mullens wasn’t even an atheist. He was suspected of maybe being an atheist and got fired.

The list of Death Cult demons is well known, scientists, MDs, atheists, liberals, gays, Moslems, other nonxians, commies, socialists, witches. The more dimwitted, if that is possible, are still putting nonwhites, Catholics, Irish, Jews, ans Slavics on their lists.

What keeps them from purging the demons from among the USA population, the upper 50% of the population is a sad fact. The US government no longer allows religious cultists to deploy heavy weapons such as tanks and artillery or field armies.

So many people to hate and kill and all the normal people get upset if a fundie machine guns a few hundred demons. Because you know, xianity is a religion of peace, love, and tolerance and jesus loves us.

I have to conclude that the reviewers were very sloppy, incompetent, or both; at the very least they were inattentive in this case, despite the editor’s claims to the contrary.

In addition, the two “well-respected and highly competent reviewers” could have handed the task of reviewing the paper to other people in their labs, who in turn did a sloppy and/or incompetent review. Furthermore, remember that this was a review paper, not a research paper, so the temptation would be to just breeze through it quickly since there were no actual experimental results to evaluate.

I’ve come across a number of scientific articles that spice things up by mentioning in passing how various properties traditionally attributed to the ‘soul’ can be made sense of in naturalistic terms. I’ve seen closely related religious topics come up as well. Libet’s classic work on neuroactivity and free will talks about a possible neurocognitive basis for Biblical prohibitions. (I don’t recall whether he uses to term ‘soul’ but it would be easy to check.)

In general, I think, we should welcome work that naturalizes whatever sensible advice or insights can be skimmed off from religious folklore. And that sort work is made easier by allowing ourselves to mention (not use!) the relevant vocabulary. It seems plausible that, in this case, the journal reviewers took the authors to be trying to do something of that sort.

If there’s a problem here, it’s surely with the way evidence was adduced in the article itself for the hypotheses that were being defended?

Speaking of persecution by Christians, there’s also a case coming to court where the ACLU is suing on behalf of a student in, I think, Oklahoma, whose school administration persecuted her because they believed that she had cast a hex on a teacher (and presumably they also believed that the hex had worked). This brief trip back to the witch persecutions of yesteryear brought to you by modern American Christians.

Off topic: I need your perceptions for an image on my blog, and I’ve put up a poll. I think I’m seeing extra soft parts in an early chordate, Pikaia. Please drop by and tell me if I’m seeing things.

@22 Nerd of Redhead: I agree with you about the value of clarity and precise definitions. But that’s why I made the distinction between *using* religious words as part of the content of one’s article and merely *mentioning* them as perhaps gesturing toward phenomena that should be explained in a more basic and more rigorous vocabulary. With time, doing the latter gives us a shot at explaining away religious doctrine.

Speaking of persecution by Christians, there’s also a case coming to court where the ACLU is suing on behalf of a student in, I think, Oklahoma, whose school administration persecuted her because they believed that she had cast a hex on a teacher (and presumably they also believed that the hex had worked). This brief trip back to the witch persecutions of yesteryear brought to you by modern American Christians.

That’s actually old. What’s more troubling is Saint Obama’s constant toadying to the religious. He’s now going further to breaking down Church-State than Bush… Which is frightening.

I was just wondering if all you scientific types could help me locate my soul. It seems that it was missing for about 4.5 billion years, has briefly entered my body, and is then likely to vanish again for all eternity. I think it has changed somewhat in that short time, but I really can’t be sure.
Has anyone seen it? Is there a soul-o-meter out there to detect it (and what coulour is it – I hope it’s not black! -errr…no, black, or mixed race, would be just fine) and when I do find it what can I do with it?
Thankyou. Concerned of England.

I was just wondering if all you scientific types could help me locate my soul. It seems that it was missing for about 4.5 billion years, has briefly entered my body, and is then likely to vanish again for all eternity. I think it has changed somewhat in that short time, but I really can’t be sure.
Has anyone seen it? Is there a soul-o-meter out there to detect it (and what coulour is it – I hope it’s not black! -errr…no, black, or mixed race, would be just fine) and when I do find it what can I do with it?
Thankyou. Concerned of England.

Do the two who I can only guess had smoked something really too good while reviewing the paper in question still have their jobs? In this economy I would not casually advocate firing anyone. On the other hand, I have to wonder what was their malfunction?

To all the trolls parsing word use, and especially to the one quoting Orwell:

Orwell wrote extensively (see the non-fiction essay at the end of 1984) about the dishonest use of words, in deliberate attempts to mislead. Try reading the entire book next time.

There exists no prohibition on the use of the word “soul.” According to the article “… the paper had four major red flags that the journal’s reviewers and editors should have caught before accepting it for publication… [emphasis mine]” A “red flag” to alert someone to the possibility that an article has something questionable or dishonest resembles a person shipped off to a re-education camp – how?

The other’s commenting here are far nicer than I am. If Warda and Han were sent to a “re-education camp” to learn how to make rational inferences from verifiable evidence I would want to be Sgt. Schultz. When they babble about an invisible creator I could answer: “I see nothing, I hear nothing, you know nothing.”

This entire episode points out a weakness in scientific peer review that creationists and other pseudoscience proponents may try to exploit again.

I wholeheartedly agree, much like this fraud of a paper which managed to get published in Nature. It was clearly fast-tracked through the peer review process without the appropriate fact checking, and the conclusions drawn are pretty weak for lack of data (mathematic functions are used to in-fill where a lot of data is missing).

Perhaps there’s something some of you can answer here ? how is it that a paper can get published without revealing the statistical methods employed so that they must be reverse engineered in order for the results to be duplicated? Why are these details protected like national security secrets which require a FOIA to reveal?

Yeah, I’m a little punchy today, but these are honest questions. Clearly the peer review process can be occasionally “slipped a mickey” so-to-speak.

Do the two who I can only guess had smoked something really too good while reviewing the paper in question still have their jobs?

It’s extremely unlikely reviewing this paper was more than a tangential part of their official duties. If you publish in peer-reviewed journals, it’s expected by the community that you take your turn at reviewing, but you don’t get paid, there’s no kudos attached, generally you remain anonymous. What’s surprising is that it’s usually done quite well.

I don’t want to get into a huge war over it, but there’s a pretty clear lack of data upon which to draw any conclusions, let alone the ones which were arrived at. I don’t think it’s appropriate to invent new statistical methods to in-fill data which does not exist in order to illustrate a trend. Also bothersome is that the instruments which collected the data weren’t checked to assure they were measuring what they were supposed to.

That paper is at the center of a lot of controversy lately. I’m not one fit to write a rebuttal since it isn’t my field, but rather an ancillary interest of mine which I do follow (like so many things these days).

I do understand the rush to publish, and that papers have a chance of aging like wine (better with age, or turn to vinegar), but I’d at least expect that the quality of the data be critically analyzed. Confirmation bias is an obvious pitfall of scientific research, but that’s what the peer review process is for. Sometimes it seems to fall flat on its face, and I am curious why that is.

I was going to post something, but Boletus (#20) pretty much beat me to it. It’s entirely possible that the reviewers could have viewed the use of the words “the soul” as poetic license. Some review articles or brevia, especially in general-interest science journals, tend to use punchy, flowery, attention-getting titles that often way overstate their case. The little News & Views things about current research can have cutesy, not-quite-accurate titles, and I notice that seeping more and more into submissions for things like Science Brevia, which has an 8-word limit to the title (though the editors do a good job in making the final changes to something more sensible). Like, to use a fictional example, “Body, Mind, and Synaptotagmin” could be changed to the more descriptive “Calcium-Dependent Regulation of the SNARE Complex by Synaptotagmin”.

I also once reviewed a paper where the author mentioned “chi” in the introduction, but the study itself wasn’t woo. We had him cut it out. The reviewers may have come across a lot of goofball cases like that, and just let it slide.

I do understand that the data was published and the concept of interpolation. You don’t need to insult my intelligence.

I’m talking about the methods employed to analyze and correct the data, not the data itself. In this case, it was eventually released, a fact of which I am aware. Understandably, the probability of errors goes up in interpolation when you’ve got small data sets.

It’s not quite the same as using interpolation over a very broad set of measurements (from provably good sources), where interpolation is likely to produce more accurate results. We’re talking about a very small handful of surface stations in an inhospitable area of the world which cannot be easily checked on. Also, the satellite data doesn’t agree and we have more of it. That’s why this paper was published to begin with, in an effort to rebut the satellite account.

That still does not answer my questions, however, it’s just being an apologist for the paper itself.

I consider myself to be a pretty good reviewer, but having seen some grossly bad other reviews on papers I’ve done – such as one where the labels in the figures and the captions to the figures didn’t match, with no notice made by the other reviewer – I’m not the least bit surprised that it got through. I’m actually more surprised that there aren’t more ID-based papers that have slipped through. People think of peer review as like a dam that keeps all the sludge at the bottom from passing, but it’s more like a filter that’s somewhat more porous at the top than the bottom.

Anyone who wants to know the real facts about Steig’s paper should take a look at
Antarctic warming is robust. Briefly, minor errors in data, not made by the authors of the paper, and making no significant difference to its findings, were discovered after publication. To call the paper a fraud, as Ward S. Denker does@33 – without attempting to justify the charge – is a barefaced lie. “Fraud”, let me remind you, is an extremely serious charge to bring against a scientist, and implies deliberate intent to deceive. You really are scum, Denker.

Where is the truth? The truth of the mitochondria’s souls or the truth of the immutability of climates is not very far away from the truth of naturalism or climate change. The truth is in the cultural wars. Atheistic tree-huggers versus religious climate change deniers. Liberals versus conservatives.

Paraphrasing Machado:

Good American,
you who come to existence
be careful.
One of both Americas (red or blue)
is going to freeze your heart

Ah, straight to the apologist blog. There is a deliberate attempt to deceive — the credit to whom the discovery of the poor data is due. I’m not “scum” for calling it like I see it. If all of the satellite data disagrees with the conclusion, then interpolation of surface station data had better be of the utmost quality.

“Extraordinary claims require extraordinary evidence.” I don’t believe this qualifies as “extraordinary” research by any stretch of the term. Perhaps my selection of the word “fraud” wasn’t particularly kind, but I did say I was being punchy this morning. I retract the term and substitute “flimsy bullshit.” instead.

My favorite review, among those my papers have received, went something like this, “I apologize for not submiting my review in a timely manner. However, I have lost the manuscript you sent for review. As I recall, it was very well written and addressed matters of scientific interest. I therefore recommend it be published without revision.” I was impresed at how well the reviewer had nailed it!

I’m not sure I’d have spotted the kookiness on the basis of the title alone. Lots of papers, especially reviews, like to sport bold, poetic or metaphorical claims. It just a part of drawing attention to it, I suppose.

But still – by the looks of things this paper is like a robot being genial and polite, only occasionally breaking into a Dalek-style EXTERMINATE, then carrying on.

Ward, what is your problem with science? Oh, other than it doesn’t necessarily agree with your preconceived notions?.

Nothing at all, so long as it’s done well. I don’t believe that it was in this particular case, nor do I believe it was in the case of the main topic at hand. My “pre-conceived notions” are based upon quite a bit of investigation into the literature on my part. This particular field of research doesn’t lend itself well to providing exacting experimental results. It’s a bit like trying to diagnose the internal conditions of a car whilst only having the data from the tailpipe emissions to go on. Some conclusions can be drawn, but they aren’t nearly so strong as if one had a full understanding of the workings of the engine.

Science is about the data and facts. Not politics.

That’s a fine observation, one with which I agree, but it’s your contention that this is about politics and not science, not mine.

Ward, if you aren’t a scientist, you are in no particular position to criticize science. As a 30+ year practitioner of science, I get very irritated with dilettantes like yourself who claim they know more than the experts. Bullshit. You need to do what I do, I listen to the experts.

I’ve been finding a much too complacent and sympathetic view of people who propagate misinformation and quack theories in my work with publishing sites. I’ve been fighting a “fact check” team who think that opinion labeled as fact is ok in science topics. They told me I have to respect other people’s opinions and that my scientific training is just one side of the story.

They supposedly don’t want to hurt anyone’s feelings, but they fail to notice just how much is at stake when you don’t correct someone who’s wrong. It’s bullshit.

Ward, if you aren’t a scientist, you are in no particular position to criticize science. As a 30+ year practitioner of science, I get very irritated with dilettantes like yourself who claim they know more than the experts. Bullshit. You need to do what I do, I listen to the experts.

You don’t know who I am or what I do. All you have is a collections of assertions about me.

When there are differing opinions, therefore, differing experts to listen to. Mine have a minority opinion, but science is not about consensus building and you know it.

Anyway, I’m not getting into an argument about it, lest I be labeled a thread-jacker, derailer, or what have you.

Ward, Science is about the facts and data, not the spin you and your political cronies try to put on it. If you expertise, write the paper and refute it. Otherwise defer to the real experts who wrote the paper. By defer, I mean shut up.

Denker is a bit of a difficult case. I’d hate to see him banned; on most topics I find his comments to be generally pretty sensible, whether I agree with them or not. But he is also a warming denialist, and once he has mounted his hobbyhorse (and it is very, very easy to get him in the saddle), he transforms from Dr Jekyll to Mr Troll. And then the thread is well and truly jacked and we have eight or nine hundred of his lunatic warming-what-warming posts.

To avoid letting him swell threads to the bursting with his tedious dishonest off-topic denialist parrot-chattering, may I suggest the following: engage with him freely when the fever isn’t upon him. But when he writes anything in the remotest way related to global warning, ignore him studiously. Leave him to emerge from the fit on his own.

Mrs Tilton is correct, and I would add that many “fits” are best dealt with by lying down and placing a paper bag over the head. I’m not a doctor, but I often pretend to be one – sometimes for financial gain – so I can attest to the efficacy of this remedy. On no account should the patient go near a computer, however, until the spasms have passed.
That’ll be $100.

Denker is a bit of a difficult case. I’d hate to see him banned; on most topics I find his comments to be generally pretty sensible, whether I agree with them or not.

Thank you for the kind words. Few enough of the kind are offered here, for whatever reason that may be.

But he is also a warming denialist, and once he has mounted his hobbyhorse (and it is very, very easy to get him in the saddle), he transforms from Dr Jekyll to Mr Troll. And then the thread is well and truly jacked and we have eight or nine hundred of his lunatic warming-what-warming posts.

To avoid letting him swell threads to the bursting with his tedious dishonest off-topic denialist parrot-chattering, may I suggest the following: engage with him freely when the fever isn’t upon him. But when he writes anything in the remotest way related to global warning, ignore him studiously. Leave him to emerge from the fit on his own.

And you started off so well, too. I asked a question, which none of you has seen fit to answer. I’ve repeatedly rebuffed attempts to put me on the defensive, and I’ve deflected obvious baiting to get me into an argument, which I don’t have any particular desire to do (which appears to be the point of #64, and I apologize in advance if this is a misinterpretation of your motives).

I consider it rather impolite to continue to discuss me in third person as if I am not here so as to elicit a response from me. Realize that I don’t go around posting any old thing I feel like, I try to stay relevant to the topic. I am frequently dragged off-topic by others. I understand well the desire to put dissenters on the defensive, but I reject it.

I’m not going to cast aspersions on your position and refer to you in third person so as to strip you of your humanity (talking as if you are a small child or family pet), and I kindly ask that you show me a similar courtesy.

Tis idiomatic that ID cannot even get into peer reviewed publication with kosher research without getting busted for their usual antics…and if it were not for the lackadaisical not to mention incompetent perusal by a couple of reviewers they would not have even got as far as they did!

For a movement that had its beginnings many years ago and that boasts scientific research as a by line there has been to date zilch paper published in any reputable science journal…

Mainly because they have none…they have nothing to test…nothing to research…their intellectual direction has produced not one thing…probably cos when confronted by a enigma they betray themselves by the inane chanting of tisgodwotwentandgoneanddidit and go no further.

What they ‘do’ have are unsubstantiated claims backed by dubious figments of fact concocted on the back of extremely rabid bias.

ID has nothing…it is nothing…just delusional dreams…that is the only message it has.

Tippy toeing around a ‘belief’ is all fine and well for the human rights brigade….but when that ‘belief’ has to resort to lies distortions to proclaim and promote itself and tries its utmost to poison real science with innuendo and the incessant whining of unfairness…it is more then time to call it quits…and expose the nonsense fully comprehensively and with no mercy what so ever after all it is the 21st century not the Salem witch trials!

To be fair at least PZ and a few notable others do…tis more then about time that more rational folks did without compunction or fear of not kowtowing to the delusion of ‘belief’ as a reasonable attitude and thus ‘protected’…

Since when have lies and deceit been given the protection of law…totally farcical..that cannot be the intention of the constitution…I cannot ‘believe” that!

Getting shot of ID would be satisfying no doubt…but not half as attractive as pulling the carpet from under the bigoted and pompous arses of the cults that infest Christianity…Christianity I do not care about…it is only those folks afflicted with it that declare it the only religion that need culling.

Time to reclaim society…

Did my bit this morning…got a fidgety creo ringing my doorbell…’are you interested in a publication called ‘the beauty of Earth’…with a big soporific grin on his face…and a ‘may I come in to discuss Jesus with you?’
I simply told him to come back when he was more rational…I do not think I will see him again!

Thanks for giving me a chuckle. I mean, that was a rather blatantly na´ve statement. Ideally, science is about data and facts. But in reality… there’s nothing we humans can do without at least some contamination by politics and personal prejudices. This is especially apparent among climate change supporters — any argument against climate change, regardless of how rigorously substantiated by hard evidence, is automatically labelled as “ultra-right-wing religious-based denialism” etc. That is a very WRONG way to approach the subject, and definitely proves the point that science is thoroughly infused with politics.

If Denker finds a problem with a paper, he has every right to present his arguments, regardless of the political climate. That does not make him ‘scum’. Obviously he is an academic of some sort, for few have full access to Nature outside academic institutions. And experts often make errors . One doesn’t have to be an ‘expert’ to point them out, provided they have sufficient evidence to back up their own arguments. The experts may sometimes even miss obvious details in their own field due to being immersed in it for too long. Fresh blood is good for progress.

Whether Denker does, in fact, have substantial evidence to back up his accusations, I don’t know. Now do I particularly care — there’s much research out there I personally find more exciting than climate change. Just my personal taste, nothing else.

But imposing certain political views on others WHILE CLAIMING THAT POLITICS IS IRRELEVANT TO SCIENCE is just plain…bullshit!

One of the most truly striking things about ID is how it didn’t manage in any way to insert itself into science. I think they genuinely thought they would – I mean, since for them Christianity lies at the heart of all things – and therefore, presumably, science – they must have imagined it wouldn’t be difficult. All you do is to employ some doctrinely sound scientists, put them to work and…well, nothing. It couldn’t just be because the likes of PZ “controlled” scientific research. It wasn’t even that science, so even their most faithful acolytes told them, was as “Expelled” represented it. Apparently, at every level, scientists were honest in a very profound way. So where, then, were Christian scientists to make their mark?
Every interesting theological specualtion they could come up with seems so damm secular!
Biology means nothing without evolution, physics is too weird and full of cheery speculation to be of any use to them, and chemistry’s just lego with molecules – where the fuck is God in it all?
Mathematics…well, yes, but…no one understands that at all, except a few nutcases who scarcely live in this world at all (and Marcus du Sautoy).
Where, then, can they look? Where is God in all this?
Nowhere, nowhere, nowhere.
Sorry.
And the atheists told you first.

Sincere apologies for having a different view on some topics from the rest of you guys. Not. And if Denker does in fact get banned for “climate change denialism”, this would speak volumes about the intellectual liberty and values of this blog community. Which is sad, because I thought I’d be able to fit in with like-minded science-loving atheists, at least. I mean, that’s already a rather miniscule proportion of the total population! Shit.

This is not a creationist blog. You do not get banned for contrary opinions, and I get so tired of the projection cranks exercise when they come here and claim they are so brave and bold, because they think they’ll get banned just for disagreeing with me.

You do get banned for being boring, obsessive, repetitive, jebus-walloping, racist skanks. Are you in one of those categories?

I actually strongly object to the implication that the reviewers should have rejected this paper because of the creationism per se. There’s creationist nonsense in there, and they should have noticed and rejected this paper because of the nonsense.

Admittedly, creationism is usually a warning sign of nonsense, but if such a thing as creationist sense exists, it should be published. Science is about following the facts, even if you don’t like the conclusion.

Of course, the full story shows that they’re pretty much incapable of writing sense of any kind; the concealing padding was all plagarized. They’ll need another Marcus Ross to write something both original and plausible.

Aside from other fallacies, I’m technically with science myself. It pays my bills, for one thing…

I’m unaware of Denker’s previous history, but he seemed reasonable on this thread. Comments like Tis Himself’s “I killfile Libertarians” do not point to a very liberal atmosphere, so naturally I had more sympathy to the victim.

There’s many ideas I disagree with feverently and even more ideas I have no current verdict on — however, I will always support the rights of those who say what I do not like, for it is not up to me to judge what’s right and what’s wrong for others. I can only make a decision for myself. Or put the decision on hold. I can try to convince others — but killfiling a whole group of people is not particularly condusive to rational discourse.

And our main problem with creationists and religious fundies is their refusal to analyse alternative ideas. Had they engaged in rational discourse with us, there wouldn’t be any fundies. Or perhaps we’d be proven wrong, though unlikely. In either case, there’d be NO conflict!

I think ‘climate change denialists’ do have valid points, as do climate change supporters. I haven’t made up my mind with whom to side, but I sure as hell believe this is the time to allow rational discourse in its utmost freedom, breaking the barriers of childish political correctness and analysing the data as it is, free of what we’d like it to be.

Since that is getting way off topic, I’ll comment on the paper:

News to me that the endosymbiotic theory of mitochondrial origin is under dispute. Endosymbiosis is pretty much an absolute fact by this point, considering we have multiple instances of secondary and tertiary endosymbiosis of the chloroplast, with quite a few transitional stages very evident. Mitochondrial endosymbiosis makes a lot of sense, and is by far more plausible than any alternative theories that have been put forth thus far.

But since they’re apparently the link between the soul and the body, hmmm… that changes things a little. What about organisms with highly reduced mitochondria? Do they have reduced souls as well? Can we trace the evolution of soul complexity and overlay it on top of the mitochondrial phylogeny? Hmmm… I think I should go write up a grant proposal…brb… XD

Godammit, PZ how do you manage to feed yourself and dependent others all day long, work, and run this blog? I mean I’ve spent several days doing nothing but blathering on Pharyngula… do you sleep? Is there a raddled picture in your attic? Have you kept quiet about a cloning experiment? What about that book you’re writing? I don’t know. It’s all very worrying.

That’s too funny to offend me. I mean, seriously… most people are offended by my complete and total irreverence to religion, or anything for that matter. Including pet political theories. Even if I agree, I refuse to revere them. That cannot be said for all atheists, as is evident here.

And that’s fine. Just… it’d be really great if we took all the accusations we throw at creationists and looked carefully if any apply to us. We would become slightly better people.

Ok, well sorry psi. I don’t know your arguments too well, but do know a few climate-change denialist arguments, and they can fuck off. Also, most cretins who come here to entertain the regulars (for a while) start off all reasonable and then within a few posts are suddenly revealed to be as mad as a bucket of frogs.
And I like saying fuck off.
On the internet, no one can punch your face in.

Sorry, John Morales, I copied the quote from Denker after having read it previously several posts above… I hold blog comments to lower fact-checking standards than my other work, sorry…

I still maintain my statement though, because the idealised science is not done anywhere. Science must be done by scientists, and as such… human error and political prejudices are injected into the system. We have a fairly decent mechanism for correcting for that, and many of us try hard to minimise error… but things do occasionally slip through. For example, the mitochondrion article.

There’s many instances of good, valid ideas being ignored for extended period of time due to not fitting in with the paradigms of their time. And this is happening right now, I could list some real example I’ve already seen in my very short time in research. Some of them are for political reasons — if not due to federal politics, then often due to discipline, department OR EVEN JOURNAL politics!

Good papers have been rejected by Nature, only to be highly praised once they ended up in one of the “lower” journals! Absolute crap has been accepted, on the other hand. Part of it is simply human error… a large part of it is due to internal politics.

It’s impossible to do science without being aware of this, and knowing how to work around it. Thereby playing your own form of politics!

Well, people just had to feed the troll and derail a potentially interesting thread.

I was hoping to read some real-life confessions about the lazy, half-assed job you did when asked to review an article that was just not that exciting, or the time you were so flattered to be contacted by that most prestigious journal that you couldn’t bring yourself to admit that you just weren’t qualified to render judgement.

But I leave disappointed, because this just never happens, does it?

Seriously, I believe that such cases are the rare exception, but I have witnessed (at a distance) the above two not-so-hypothetical scenarios. And I would bet many of you have, too.

Comments like Tis Himself’s “I killfile Libertarians” do not point to a very liberal atmosphere, so naturally I had more sympathy to the victim.

I killfile libertarians because I have a strong prejudice against them. I won’t bore you with the details as to why I have this prejudice other than to note that I’m a professional economist who gets very tired of libertarians proclaiming how von Mises and Hayek were economic geniuses and nobody else (except Milton Friedman) is worth paying attention to. In fact that wouldn’t be so bad, except the libertarians don’t even understand Mises, Hayek and Friedman.

Regardless, so that I don’t drag threads into discussions of libertarianism, I have a personal policy of killfiling all libertarians. Incidentally, this does not mean I killfile people I disagree with politically. CHK-TX brags about his conservatism and how stoopid us lieburls are but I haven’t killfiled him.

So if you’ve got sympathy for Denker because I killfiled him, that’s your privilege. Just be aware that I do it more for the other people here than for my disdain.

I’m not a denialist per se; as I’ve said earlier — merely a ‘neutralist’. I really don’t know yet, and I would like to make my own rational discision without the involvement of political correctness and such.

And I’m not about to transform into a mad ribbeting mass, I assure you =P I’m a regular lurker, posted before a few times. I just don’t like seeing ideas shut out merely due to political unfavourability. Conversely, I don’t like seeing ideas being rooted for based on political climate alone. Especially among people who claim to support freethinking.

Steve_C, good to know I can get boring after about 3 posts. Must be a special skill I have. You’re the first person to point it out, so kudos to you! Generally people have called me anything BUT boring, so it’s refreshing to receive a new insult! Cheers!

I did want to point out I’m quite impressed with PZ’s awareness of Reclinomonas and Paulinella in the post a year ago on this paper. Few people are aware of the second instance of primary chloroplast endosymbiosis, let alone the core Jakobids! The large, intact mitochondrial genome in Reclinomonas is in fact some good evidence for rooting the Eukaryote tree there. I find that kinda exciting! (ok, I’m obsessed with protists but nyeh =P)

Way back at Comment 21 Monado, FCD thought he was seeing things. I followed his link and thought I saw things too.

Ferinstance, the site pictures pikaia next to a more modern notochord. Problem being that’s head was at one end and the fossil one was at the other. I’f I’m missing something this basic, I can’t judge that Monado was asking.

PS – Someone claimed WSD was usually quite sensible. I think they are seeing things also.

I’m not going to cast aspersions on your position and refer to you in third person so as to strip you of your humanity (talking as if you are a small child or family pet), and I kindly ask that you show me a similar courtesy.

Well then, Mr. Denker, how do you suggest that Mrs. Tilton approach talking about you without using the third person? If she’d wanted to talk to you, I have no doubt that she would have risen to the occasion and utilized the second person in doing so.

Your “strip you of your humanity” whine is drama-queen bullshit. Get a grip.

When someone stoops to referring to you as “it”, then come talk to me. I’ll be in your corner.

seems like biology journals will henceforth have to apply automated global word processing operations […] to all new submissions.

No.
The reason given (For some reason, though, “neither picked up the references to creationism, nor did they recognize that sections of the text were plagiarized,” according to Dunn.) could just as well apply to the output of such automation as to the source.

Surely we want human judgement to be the final decider on whether to publish. Here, it seems a case of error of judgement.

Comments like Tis Himself’s “I killfile Libertarians” do not point to a very liberal atmosphere, so naturally I had more sympathy to the victim.

A killfile is one user’s personal client-side filter. You can cry about it, but it just means that:

You serious? I’m whining now?

Yes, you’re definitely whining when you start complaining about the atmosphere after one person mentions in passing that they put a couple of repetitive, annoying, threadjacking trolls into a filter. Surely if you can calm down you can see that was whining, and let it go. We don’t respond well to a persecution complex.

I think ‘climate change denialists’ do have valid points, as do climate change supporters. I haven’t made up my mind with whom to side, … I’m not a denialist per se; as I’ve said earlier — merely a ‘neutralist’. I really don’t know yet, and I would like to make my own rational discision without the involvement of political correctness and such.

The fact that you think both sides are making valid points, the fact that you think there even can be two valid sides to an empirical question, the fact that you think there’s “political correctness” at play in peer reviewed hard science, the fact that you aren’t a climatologist yet you think your incredulity counts for more than the consensus of experts in the field, all reveal you as a narcissist and an Intelligent Design Creationist. Teach the controversy! The fossils say no!

I’m not “scum” for calling it like I see it. If all of the satellite data disagrees with the conclusion, then interpolation of surface station data had better be of the utmost quality.

“Extraordinary claims require extraordinary evidence.” I don’t believe this qualifies as “extraordinary” research by any stretch of the term. – Ward S. Denker

I called you “scum” for accusing scientists of fraud, without evidence. I stand by that characterisation and I don’t give a shit how “punchy” you were feeling. Your use of the term clearly indicates the contempt you have for science that contradicts your ideological presuppositions.

It is telling that you refer to RealClimate as an “apologist” site. What it is, of course, is a site run by climate scientists (including some authors of the paper), unlike the denialist blogs you doubtless frequent.

You are of course quite entitled to call attention to what you perceive as problems with the paper, just as the sane among us are quite entitled to say you’re an ignorant ideologue and we provisionally prefer the opinion of the authors (much-published climate scientists), the reviewers, and the editor of Nature. (For anyone who doesn’t know, this paper was featured on the front cover of Nature, so it will have been subjected to even more scrutiny that Nature papers usually receive.) It does, of course, take account of the satellite data – it is specifically an attempt to make use of all available data. Satellite data alone, according to NASA, indicates a warming in West Antarctica over the past 25 years (the paper’s reconstruction shows East Antarctica as cooling slightly); and over this period no data infilling was done. The infilling used the relationship between the terrestrial station data and the wider picture in Antarctica as revealed by the satellite data, to infill the wider picture from before the era when satellite data was available, and thus deduce that West Atlantic warming probably goes further back in time. If there are significant scientific problems with the paper, no doubt they will be raised in comments published in Nature itself. Maybe we’ll find the name “Ward S. Denker” among the published comments, and – GOOD GRIEF! A squadron of pigs just flew past my window!

Psi Wavefunction,I’m unaware of Denker’s previous history, but he seemed reasonable on this thread.
You think accusing scientists of fraud without evidence is reasonable? Pfft.

I think ‘climate change denialists’ do have valid points

Such as? Come on, be specific, and back up your claims.

I mean, seriously… most people are offended by my complete and total irreverence to religion, or anything for that matter. Including pet political theories. Even if I agree, I refuse to revere them. That cannot be said for all atheists, as is evident here.

“The fact that you think both sides are making valid points, the fact that you think there even can be two valid sides to an empirical question, the fact that you think there’s “political correctness” at play in peer reviewed hard science, the fact that you aren’t a climatologist yet you think your incredulity counts for more than the consensus of experts in the field, all reveal you as a narcissist and an Intelligent Design Creationist. Teach the controversy! The fossils say no!”

You serious?

Wow. Incredible.

And you, my friend, are a politically indoctrinated religious nut who will not step aside from your own views for half a second…awww fuckit, no hope for the likes of you.

I’m a creationist? ROFL. Your tax dollars fund my bills and my food through NSF. Yes, I have a job in biological research. I’m at loss of words… I mean, I’m across the hall from a world leading expert on endosymbiosis. We seem to get along pretty well. Clearly I am an Intelligent Design Creationist. Damn, you found me out.

You clearly showed you don’t work in the science industry, simply by being unaware (or in denial) of the realities of peer review.

Actually, honestly… fuckit. I’m a regular reader of this blog, but as soon as I open my mouth the entire readership seems to attack me in droves, despite the fact that I’m more or less ON YOUR SIDE.

The amount of strawmen and non-sequiturs, followed by an incredible ad hom… speak volumes about you.

Although a part of me says you’re being sarcastic. Otherwise, DOES NOT COMPUTE springs to mind.

Ha ha only serious, IDC Wavefunction. Listen, I grasp that you literally accept the evidence for biological evolution. It’s a metaphor, one that I too generously hoped you would not be too dense to notice.

The fact that you think both sides are making valid points: intelligent design creationists do this, because of their own ignorance and narcissism.

The fact that you think there even can be two valid sides to an empirical question: intelligent design creationists do this.

The fact that you think there’s “political correctness” at play in peer reviewed hard science: all creationists and anti-vaccinationists do this, because of their reflexive conspiracy theorizing.

The fact that you aren’t a climatologist yet you think your incredulity counts for more than the consensus of experts in the field: substitute biologist for climatologist and all creationists do this, because of their narcissism. There’s the metaphor, and I think it an apt one.

No, I don’t literally think that you believe in special creation, or irreducible complexity, or humans putting saddles on dinosaurs. Really, I would think the leap from “denies AGW” to “believes IDC” was large enough that you might suspect “maybe there’s a subtext here.”

But you are reasoning exactly like a creationist. You deserve to be lumped in with them. Teach the controversy!

You clearly showed you don’t work in the science industry, simply by being unaware (or in denial) of the realities of peer review.

Back up. I didn’t say that one or two or ten peer reviewed papers couldn’t be wrong. I didn’t say it was a flawless process.

But anthropogenic global warming, like biological evolution, is supported by the findings of thousands and thousands of separate studies now. Your incredulity cannot be justified by the data. This is not 1870s biology or 1980s climatology.

To distort the field as comprehensively as you imply would require massive, deliberate collusion, a vast conspiracy involving scientists from multiple disciplines, the sort of thing that creationists accuse of the whole fields of biology, geology, astrophysics, etc. Yet:

And you, my friend, are a politically indoctrinated religious nut who will not step aside from your own views for half a second

At least five times now in this thread, you have accused anyone who understands the evidence for AGW of being indoctrinated in political correctness. I don’t know why, but you appear married to this conspiracy theory. Let’s hear it. Explain in detail, using my own words as evidence, why I’m a “politically indoctrinated religious nut.” All you’ve done yet is lob those ad hominems you so hypocritically complain about. (I’ve no problem with personal attacks, mind you, but I delight in your hypocrisy.)

I’m a regular reader of this blog, but as soon as I open my mouth the entire readership seems to attack me in droves, despite the fact that I’m more or less ON YOUR SIDE.

That’s mostly because you walked in wearing a Cloak of Martyrdom +6. If you aren’t a narcissist, then you can shed the persecution complex.

thank, you yes, that’s exactly right. I am not talking to Denker here; I am talking to everybody else about him. I won’t talk to him at all when he is in denialist mode, and I urge everybody else to adopt the same policy.

And that is not as much for the content of his religious beliefs as for their inappropriateness to this forum. If this website were called “PZ’s Warming-Denialist vs. Climate-Scientist Internet Debating Chamber”, Denker’s denialism would be just as tedious and stupid, but one could hardly object to him posting it. But that is not what this website is, and it is most certainly not what this thread is. Yet here, once again, he has tried (not altogether without success) to hijack a thread that has nothing to do with his beliefs.

We should pause to ask ourselves why he would do that. Was he hoping we’d all say, “Golly Ward, we never thought about it that way before. But now that you’ve drawn that entirely legitimate comparison for us, we see that the Nature article and indeed the entire massed corpus of climate science is exactly like a article claiming that mitochondria are the link between body and soul. Ergo global warming is all a giant fraud. Thank you for helping us see the light, O Great Teacher!” Well, he doesn’t seem a stupid man, so I doubt he holds out much hope of that. No, he knows full well that he is going to be showered with brickbats and banana cream pies every time.

And I think that is exactly what he wants. Maybe it makes him feel like a brave and lonely defender of Truth assailed on all sides by the ignorant. Maybe he just likes the attention. That is, at bottom, the unifying factor underlying all internet trolls: they have never managed to comprehend that not all attention is good attention.

Now, Denker is a whack-job about warming, but he is not a one-note whack-job like so many of the people who mistake this website for Art Bell’s microphone. If his denialism comments were all he ever posted, banishment to the dungeon would be more than justified. Life’s just too short. But I meant it when I said I hope he won’t be banned, because he does post comments on other topics, and even where I disagree with him in those areas, he seems quite “normal” when discussing things other than global warming. If he persists in threadjacking and street-corner soap-box preaching, I wouldn’t be surprised to see PZ ban him some day. But if we all scrupulously refrain from responding to his denialist comments, he’ll pretty soon stop making them. In that way he’ll be in no danger of the dungeon; the threads will be freer of unsolicited antiscience gunk; and Denker will continue to be able to participate in the many conversations where his contributions are sometimes positive and in any event neither off-topic nor unwelcome. A “win-win situation”, as I believe it’s called.

On a completely different matter, may I just say that Knob Goblin’s nym made me snort a pint of tea through my nose.

You made a dramatic entrance to this thread back in post 78, defending someone obviously held in low regard by many. You ended the post with a bit of high melodrama:

(accusations of ultra-right-wing fundamentalism in 3…2…1…)

The next post, #79, was on a different topic. Then you came roaring back with post #80, opening with

Oh shit, am I under risk of being banned now too?

It seemed like the villainous landlord had told you to pay the rent or surrender your nubile daughter to his vile embrace. Except that nobody had responded to your opening salvo. You anticipated your cue. Snidely Whiplash wasn’t on stage yet.

In post #81, a respected regular, John Morales, gave a mild-manner explanation as to why Ward S. Denker is appreciated. Then, in post #83, the blogmeister himself showed up. You had just made two posts but already attracted the attention of Papa Zulu. He noted that you were whining about something that only existed in your imagination and gave you general guidance on how to get yourself banned if that was your intention. As a college professor, PZ has dealings with immature adolescents and knows how to appropriately deal with dramatic gestures.

At that point you ran around, spouting how you weren’t a creationist, in fact you did something biological, that I was a meanie for killfiling Denker, that climate change wasn’t a done deal, etc.

Finally John Morales, acting as a responsible adult, made the following post (#97):

Psi, relax. I’m of the opinion you’d be an asset to the comments, if you’d just be topical rather than engage in self-justification.

Good comment @85, when you got on topic, BTW.

Unfortunately, you’ve disregarded John’s advice. So let me put it another way. If you want to be treated like an adult then act like one. If you want to be treated like a spoiled brat, we can handle that as well. Your choice.

Psi, you’re pretty much going to get flamed when you present long arguments here which you know are “controversial” – pharyngulawise.
And you’ll definitely get insulted when you start accusing mainstream science of being political. It can be used that way, I guess, but scientists, almost without exception see their work as, by definition non-political and non-religious. There’s no agends, just a desire to look more clearly at what we think of as universal truth.
Climate change is just one such issue.
There are plenty of sites where you can share your concerns with sympathetic others. This isn’t one of them. We can be very nasty here, and if you don’t want that well…you know what to do.
Oh, and as I said, try to keep those posts short!

While I understand what you’re trying to do, and appreciate it, it’s kind of a “deaf ears” crowd.

They’ve got ideological blinders on which prevent them from seeing the obvious. To them, AGW skeptics are “denialists” and are equal to creationists.

I’ve tried to explain the difference before (that it’s a difference in scientific opinion) but they refuse to accept that. Creationism is easy to reject as a scientific pursuit — they can’t form a testable, falsifiable hypothesis. That’s no small distinction.

Well then, Mr. Denker, how do you suggest that Mrs. Tilton approach talking about you without using the third person?

There’s no reason to talk about others at all. It’s generally better to stick to addressing concerns to an individual, otherwise it ends up becoming an “us vs. them” situation, and it’s hard not to take that personally.

Also, my original post wasn’t a thread derail. There were two main themes of PZ’s post. The first was talking about a specific paper, and the second was incredulity about the fact that the paper should obviously not made it past peer review. I addressed the second topic with another paper I feel qualifies under that category.

I wasn’t aware that your opinions were so fragile as to require special care. I shall endeavor to coddle your egos as much as possible in the future. Lord Keynes and Team AGW need more sycophants, surely.

Ward, I am familiar with pretentious posing pseudo-intellectuals like yourself. I have met many of them over the years with no joy. And guess what, they don’t appear so intelligent to other people. Science rules over opinions of dilettantes such as yourself.

I’ve tried to explain the difference before (that it’s a difference in scientific opinion) but they refuse to accept that. – Denker

That’s because it’s a barefaced lie. Just as you can find the odd qualified biologist who is a cdesign proponentsist, the odd geologist who denies continental drift, and the odd virologist who denies that HIV causes AIDS, you can find the odd climate scientist who denies the reality or seriousness of AGW. The scientific consensus is just about as strong in the last case as in all the others. The denialists in each case resort to cherry-picking, constant repetition of already-refuted talking points, accusations of fraud and ulterior political or financial motives, denunciations of “groupthink” and consensus, and of course, misrepresentation of the state of the scientific debate which in reality is, in each case, effectively over. In any of those cases, the debate conceivably could be reopened by new findings, but no-one who isn’t an idiot or ideologue expects it.

They’ve got ideological blinders on which prevent them from seeing the obvious.

Yes, tell us more about this vast conspiracy theory. Give us the red pill.

I’ve tried to explain the difference before (that it’s a difference in scientific opinion)

It’s primarily a difference between climatologists and non-scientists… but that’s not what you’d like to imply.

Creationism is easy to reject as a scientific pursuit ? they can’t form a testable, falsifiable hypothesis. That’s no small distinction.

False as usual. Intelligent design creationism is testable and falsifiable. That’s what Behe’s black box and irreducible complexity is all about. And it has been falsified.

There’s no reason to talk about others at all. It’s generally better to stick to addressing concerns to an individual, otherwise it ends up becoming an “us vs. them” situation, and it’s hard not to take that personally.

You disrespect everyone else here by trolling every single thread and turning it into a discussion about you and your pet issue. Why should anyone respect you in return?

I addressed the second topic with another paper I feel qualifies under that category.

Which just happened to be the only thing you ever talk about.

Lord Keynes and Team AGW need more sycophants, surely.

Oh good, an expansion of your conspiracy theory. Keynesians, operating through the United Nations, invented anthropogenic global warming, in order to destroy the world economy, for the benefit of developing nations. The same developing nations which resist carbon reduction proposals, but it’s a conspiracy theory so there’s no reason to be consistent.

At the moment, I can only download the abstract and figures (both of them, simple diagrams at that), but I can safely say that this is yet another data-free piece of tripe from Chaos, Solitions & Fractals.The second time it’s happened, in fact. The dead giveaway is that the author is discussing a “new paradigm” in biology in…a non-biological journal. Seriously, this journal needs to stop publishing papers that purport to be about biology, they’re embarrassing themselves.

For fuck’s sake, why are you discussing AGW? It’s not in the subject, it’s not a topic that most people here are interested in talking about, and it’s not something that will produce much more than insults from the pro-scientists (well, and some well-written rebuttals). I don’t go on Christian sites and bring up my hobby horses – why are you doing it here?
Yes, we’re all closed-minded drones, no we don’t know the latest “research” which supports your hypothesis, and we don’t care. Why bother raising it at all, other than to happily prove your own self-fulfilling prophecy.
If you wait long enough, there’ll be anothother global warming thread where your opinions might be of interest, or even called-for, but I’m afraid that you’ve just justified exactly what Mrs T said on no.64.

One good thing to come out if this: I had a paper under review in this journal (Proteomics) at the time. I withdrew it and sent it elsewhere as a result of Dunn’s refusal to be open about this.

Now if only he would actually reveal whether the “competent” reviewers in question have been struck off the editorial board, some confidence might be forthcoming. It will be interesting to watch the impact factor of the journal fall lower as confidence decreases due to things like this.

You think this is bad though… I have some stories about other journal editorial practices that will make your skin crawl!

Psi, the very fact that Denker claims Steig was using the AWS numbers to refute the satellite numbers is evidence he didn’t bother to either read the paper or read Steig’s explanations of the paper. Steig et al. used the satellite data and used information from both the manned and unmanned stations as a means of verifying the satellite data.

That is why in my second post I asked him what the AWS data was used for. He seems to think it was the primary source and used specifically to counter satellite data that shows cooling. Steig’s explanation shows otherwise, the eastern 2/3 of Antarctica is cooling but at an insignificant level while the western 1/3 is warming at a significant level. Taken as a whole, rather than just focusing on the 2/3s that is cooling as Denker appears to be doing, indicates that the Antarctica is warming.

What you did here is lie by omission. You deliberately misquoted me, omitting the part you could not disprove. ID Proponents do this all the time with Darwin’s words.

I’ve tried to explain the difference before (that it’s a difference in scientific opinion) but they refuse to accept that. Creationism is easy to reject as a scientific pursuit ? they can’t form a testable, falsifiable hypothesis. That’s no small distinction.

False as usual. Intelligent design creationism is testable and falsifiable. That’s what Behe’s black box and irreducible complexity is all about. And it has been falsified.

The ID hypothesis is basically “Things look like they are designed (they can’t arise through natural processes),” therefore “an intelligent agent (God) did it.”

The first part presupposes that there is a designer and the second part is the achilles heel to the whole argument. One cannot test a supernatural creator and one cannot disprove it either (proving a negative). It fails to meet scientific rigor on both elements.

The ID hypothesis is basically “Things look like they are designed (they can’t arise through natural processes),” therefore “an intelligent agent (God) did it.”

The first part presupposes that there is a designer and the second part is the achilles heel to the whole argument. One cannot test a supernatural creator and one cannot disprove it either (proving a negative). It fails to meet scientific rigor on both elements.

You are embarrassingly wrong. I never thought I would say this to someone, but maybe you should read Darwin’s Black Box. You aren’t arguing against it effectively, because you don’t understand the claims.

The argument from irreducible complexity is, roughly:

1 every step in an evolutionary history is subject to natural selection (empirical, uncontroversial)

2 if a mutation is not adaptive, it will not persist in the genome (empirical, false, ignores neutral theory)

3 most complex structures are monumentally unlikely to have arisen in a single mutation (empirical, uncontroversial)

4 certain of these structures, like the bacterial flagellum, become useless if any one of their component parts are removed (empirical, false, see Ken Miller’s rebuttals on flagella and mousetraps)

5 therefore these structures could not have evolved, because the intermediary steps would not have persisted in the genome (empirical, false from 2 and 4)

6 since these structures could not have evolved, there must be some other explanation; intelligent design is the most parsimonious explanation left (empirical, but false since 5 is false)

Nothing requires that the intelligent designer be supernatural, which is why the Raelians have adopted this argument. Every step in the argument is an empirical claim. Several of those empirical claims have already been falsified, but you are painfully wrong to assert that it is not testable or falsifiable.

There is no epistemological distinction between AGW denial and ID. Both are testable, both are wrong, and you are just like an intelligent design creationist.

Nothing requires that the intelligent designer be supernatural, which is why the Raelians have adopted this argument. Every step in the argument is an empirical claim. Several of those empirical claims have already been falsified, but you are painfully wrong to assert that it is not testable or falsifiable.

This is where your argument falls down. It does not matter whether the “designer” is supernatural or not, but evidence for its existence must be presented.

Say that the “designer” is a long-dead (or far distant) species of aliens. If we have absolutely no evidence for their existence, we cannot come to a conclusion one way or another. It becomes an untestable hypothesis (just as if we concluded the creator was a leprechaun, invisible pink unicorn, FSM, or celestial teapot). Science does not get into the business of proving a negative. Science seeks natural solutions, ones supported by empirical evidence.

If you’d like to try and explain why it is you think that the conclusion is testable, I’m all ears, but stop slagging on me, else this conversation is at its end.

You are perpetually stupid, Ward. It is becoming apparent that you cannot work in science or even philosophy.

This is where your argument falls down. It does not matter whether the “designer” is supernatural or not, but evidence for its existence must be presented.

(I’m just going to pretend to be an ID creationist for the moment because it’s grammatically easier than adding a caveat to every statement.)

The existence of bacterial flagella, which could not have evolved, is the evidence for a designer. Like all natural phenomena, the flagellum requires an explanation. Because it is irreducibly complex, evolution by natural selection cannot explain the flagellum. What are the alternative explanations? Are there any explanations besides design and evolution? If not (and honestly, to my knowledge, no one has suggested other explanations), then with evolution crossed off the list of possibilities, only intelligent design remains. Unless and until someone offers a third possibility, intelligent design remains the most parsimonious explanation of the flagellum.

It is not immediately necessary to identify the designer. When Mendel put forward his theories of genetics, for instance, it was not necessary for him to identify DNA. He did not have any solid evidence for a genetic chemical; he only had inferences. That did not make his work unscientific. The luminiferous aether was never found, but that did not make the hypothesis unscientific, just wrong.

Here is Ken Miller, Eugenie Scott, and several other scientists saying you are wrong.

me: you’re appealing to authority.
Ward @138:

Nonsense. I appealed to an authority we both accept […] That distinctly puts it in the category of not a fallacy.

Really.

What you’ve done is avoided putting forth an argument to knob goblin’s contentions, instead interpreting your own gist and responding to that by saying goblin is wrong because some scientist has said something that addresses your perceived gist.

Then you said the conversation was at an end; I suspect because addressing goblin’s contentions is beyond you.

KENNETH R. MILLER (Dramatization): If you invoke a non-natural cause, a spirit force or something like that, in your research, I have no way to test it.

WITOLD “VIC” WALCZAK (Dramatization): So supernatural causation is not considered part of science?

KENNETH R. MILLER (Dramatization): Yeah. I hesitate to beg the patience of the Court with this, but being a Boston Red Sox fan, I can’t resist it. One might say, for example, that the reason the Boston Red Sox were able to come back from three games down against the New York Yankees was because God was tired of George Steinbrenner and wanted to see the Red Sox win. In my part of the country, you’d be surprised how many people think that’s a perfectly reasonable explanation for what happened last year. And you know what? It could be true, but it certainly wouldn’t be science. It’s not scientific, and it’s certainly not something we can test.

Mm hmm. And that’s Ken Miller talking about the supernatural version of intelligent design. Taking for granted his ontological classifications, that’s still irrelevant. Supernatural ID is not at all what I’m talking about here, as I’ve already made perfectly clear. (You really suck at this, Ward.)

Miller, by the way, endorses Gould’s nonoverlapping magisteria. I rather agree with Dawkins that it’s a too pretty overture to theists like Miller who greedily embrace it. From When Religion Steps on Science’s Turf and The God Delusion:

A universe with a supernatural presence would be a fundamentally and qualitatively different kind of universe from one without. The difference is, inescapably, a scientific difference. Religions make existence claims, and this means scientific claims.

The difference between the two hypothetical universes could hardly be more fundamental in principle, even if it is not easy to detect in practice. And it undermines the complacently seductive dictum that science must be completely silent about religion’s central existence claim. The presence or absence of a creative super-intelligence is unequivocally a scientific question, even if it is not in practice – or not yet – a decided one. So also is the truth or falsehood of every one of the miracle stories that religions rely upon to impress multitudes of the faithful. Did Jesus have a human father, or was his mother a virgin at the time of his birth? Whether or not there is enough surviving evidence to decide it, this is still a strictly scientific question with a definite answer in principle: yes or no. Did Jesus raise Lazarus from the dead? Did he himself come alive again, three days after being crucified? There is an answer to every such question, whether or not we can discover it in practice, and it is a strictly scientific answer. The methods we should use to settle the matter, in the unlikely event that relevant evidence ever became available, would be purely and entirely scientific methods. To dramatize the point, imagine, by some remarkable set of circumstances, that forensic archaeologists unearthed DNA evidence to show that Jesus really did lack a biological father. Can you imagine religious apologists shrugging their shoulders and saying anything remotely like the following? ‘Who cares? Scientific evidence is completely irrelevant to theological questions. Wrong magisterium! We’re concerned only with ultimate questions and with moral values. Neither DNA nor any other scientific evidence could ever have any bearing on the matter, one way or the other.’ The very idea is a joke. You can bet your boots that the scientific evidence, if any were to turn up, would be seized upon and trumpeted to the skies.”

There is something dishonestly self-serving in the tactic of claiming that all religious beliefs are outside the domain of science. On the one hand, miracle stories and the promise of life after death are used to impress simple people, win converts, and swell congregations. It is precisely their scientific power that gives these stories their popular appeal. But at the same time it is considered below the belt to subject the same stories to the ordinary rigors of scientific criticism: these are religious matters and therefore outside the domain of science. But you cannot have it both ways.

Collecting data from the thousands of irreducibly complex biological structures (snerk) could give us reliable inferences about what sort of tools the designer used. There’s a ready dataset in well known jokes about “unintelligent design,” as of lower back pain in bipedal humans; these can tell us about the designer’s skill level. The superiority of cephalopod eyes suggests that mammals were just practice on the way to the creation of the designer’s true chosen people, the giant squid.

And what’s this crap about a supernatural creator, anyway? A being that intervenes in our universe, in special creation or tweaking of DNA, is by definition natural and its effects empirical. This is irrelevant to my earlier example, regarding uncontroversially natural extraterrestrials, but for the record I don’t recognize the supposed dichotomy.

But, since you persist in slagging, true to my word, this conversation is at its end.

Don’t hope for a moment that I’ll miss your company, you fanatical conspiracy theorist. Insulting you has been the only way to keep this interesting. You’re rather too dull for a thoroughly serious discussion.

Inasmuch as “soul” is used synonymously with “spirit”, which is related to breath as in “respiration”, is it possible that the Warda and Han thing actually started out as a review on mitochondria and respiration (which makes sense) and then got derailed by a rogue thesaurus?

Knob goblin is of course right: creationism in its original form was disproved empirically, back in the 19th century. When Behe claims that the bacterial flagellum, or the vertebrate blood-clotting system are “irreducibly complex”, those are empirically falsifiable – and indeed, falsified, claims. Go and look at the denialism blog: there is ample documentation there of the fact that AGW denialism shows exactly the same pathologies as creationism, HIV-AIDS denialism, etc. Your claim that it is a difference of scientific opinion is, I repeat, a barefaced lie.

Our inclination is to categorize the most frequent and kinetically favourable interactions as the right ones and the minor ones as tolerable errors, but in the absence of any grand designer102 there are no right or wrong interactions ? just handholds of different sizes that selection can use to climb a fitness mountain.

I am quite surprised that nobody comments on the usual habit of respectable journals (such as Proteomics) to publish, as a rule, only invited reviews. Proteomics does have this rule in their current Instructions for authors (revised December 2008). I wonder whether (i) the rule was included in consequence of the Warda/Han scandal (not very likely), or (ii) they actually invited Warda and Han, or (iii) the paper was pushed in as an uninvited review against the rule, which should have been another red flag.

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